Starting phenix.real_space_refine on Wed Sep 25 15:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/09_2024/6qno_4598_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/09_2024/6qno_4598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/09_2024/6qno_4598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/09_2024/6qno_4598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/09_2024/6qno_4598_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/09_2024/6qno_4598_neut.cif" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6647 2.51 5 N 1718 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10429 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1711 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain breaks: 2 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2392 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 306} Chain: "G" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 293 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "L" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "H" Number of atoms: 1660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} bond proxies already assigned to first conformer: 1692 Chain: "R" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2646 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N SER L 42 " occ=0.94 ... (4 atoms not shown) pdb=" OG SER L 42 " occ=0.94 residue: pdb=" N SER H 176 " occ=0.54 ... (7 atoms not shown) pdb=" OG BSER H 176 " occ=0.34 residue: pdb=" N GLN R 64 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN R 64 " occ=0.50 residue: pdb=" N TRP R 161 " occ=0.50 ... (12 atoms not shown) pdb=" CH2 TRP R 161 " occ=0.50 residue: pdb=" N PHE R 313 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE R 313 " occ=0.50 Time building chain proxies: 7.65, per 1000 atoms: 0.73 Number of scatterers: 10429 At special positions: 0 Unit cell: (90.47, 117.86, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1986 8.00 N 1718 7.00 C 6647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.04 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 167 " - pdb=" SG CYS H 222 " distance=2.04 Simple disulfide: pdb=" SG CYS R 2 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 15 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 17 sheets defined 28.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.734A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.038A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.510A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.793A pdb=" N CYS G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.539A pdb=" N ASN G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 removed outlier: 3.535A pdb=" N GLY L 153 " --> pdb=" O GLN L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 213 Processing helix chain 'H' and resid 72 through 75 removed outlier: 4.437A pdb=" N GLY H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 213 through 218 removed outlier: 3.864A pdb=" N SER H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 65 removed outlier: 3.543A pdb=" N PHE R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Proline residue: R 53 - end of helix removed outlier: 3.598A pdb=" N HIS R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 69 removed outlier: 4.143A pdb=" N ARG R 69 " --> pdb=" O LYS R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 66 through 69' Processing helix chain 'R' and resid 73 through 101 removed outlier: 3.541A pdb=" N LEU R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 141 removed outlier: 3.508A pdb=" N GLY R 109 " --> pdb=" O PHE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.814A pdb=" N ALA R 153 " --> pdb=" O GLY R 149 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 199 through 212 removed outlier: 3.832A pdb=" N PHE R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 237 removed outlier: 3.509A pdb=" N GLN R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 278 removed outlier: 3.620A pdb=" N GLN R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 284 through 306 removed outlier: 3.923A pdb=" N ILE R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix Proline residue: R 303 - end of helix removed outlier: 3.579A pdb=" N TYR R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 319 removed outlier: 5.528A pdb=" N CYS R 316 " --> pdb=" O GLN R 312 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.513A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.622A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.979A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 4.085A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.952A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.714A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 7.062A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AB1, first strand: chain 'L' and resid 78 through 79 removed outlier: 3.521A pdb=" N ASN L 78 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN L 70 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR L 74 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU L 58 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 139 through 143 Processing sheet with id=AB3, first strand: chain 'L' and resid 178 through 179 Processing sheet with id=AB4, first strand: chain 'H' and resid 22 through 26 removed outlier: 5.604A pdb=" N GLY H 35 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU H 98 " --> pdb=" O CYS H 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.074A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 147 through 151 removed outlier: 6.457A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU H 201 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU H 197 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR H 203 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA H 195 " --> pdb=" O THR H 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 178 through 181 Processing sheet with id=AB8, first strand: chain 'R' and resid 178 through 181 removed outlier: 4.261A pdb=" N SER R 186 " --> pdb=" O GLU R 181 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3215 1.34 - 1.46: 2756 1.46 - 1.59: 4591 1.59 - 1.71: 5 1.71 - 1.83: 113 Bond restraints: 10680 Sorted by residual: bond pdb=" C6 RET R 401 " pdb=" C7 RET R 401 " ideal model delta sigma weight residual 1.459 1.657 -0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C8 RET R 401 " pdb=" C9 RET R 401 " ideal model delta sigma weight residual 1.450 1.593 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C10 RET R 401 " pdb=" C11 RET R 401 " ideal model delta sigma weight residual 1.433 1.548 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C14 RET R 401 " pdb=" C15 RET R 401 " ideal model delta sigma weight residual 1.448 1.536 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C12 RET R 401 " pdb=" C13 RET R 401 " ideal model delta sigma weight residual 1.446 1.534 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 10675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13645 2.42 - 4.84: 719 4.84 - 7.27: 106 7.27 - 9.69: 23 9.69 - 12.11: 5 Bond angle restraints: 14498 Sorted by residual: angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" C GLN A 204 " pdb=" N ARG A 205 " pdb=" CA ARG A 205 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C LYS R 311 " pdb=" N GLN R 312 " pdb=" CA GLN R 312 " ideal model delta sigma weight residual 120.38 126.94 -6.56 1.46e+00 4.69e-01 2.02e+01 angle pdb=" CA GLU A 43 " pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 114.10 122.49 -8.39 2.00e+00 2.50e-01 1.76e+01 angle pdb=" CA TYR R 301 " pdb=" CB TYR R 301 " pdb=" CG TYR R 301 " ideal model delta sigma weight residual 113.90 121.38 -7.48 1.80e+00 3.09e-01 1.73e+01 ... (remaining 14493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 5828 15.88 - 31.76: 406 31.76 - 47.64: 73 47.64 - 63.52: 12 63.52 - 79.39: 8 Dihedral angle restraints: 6327 sinusoidal: 2470 harmonic: 3857 Sorted by residual: dihedral pdb=" CA PHE H 173 " pdb=" C PHE H 173 " pdb=" N PRO H 174 " pdb=" CA PRO H 174 " ideal model delta harmonic sigma weight residual 180.00 125.94 54.06 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA TRP R 175 " pdb=" C TRP R 175 " pdb=" N SER R 176 " pdb=" CA SER R 176 " ideal model delta harmonic sigma weight residual 180.00 -127.18 -52.82 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO R 327 " pdb=" C PRO R 327 " pdb=" N LEU R 328 " pdb=" CA LEU R 328 " ideal model delta harmonic sigma weight residual 180.00 130.79 49.21 0 5.00e+00 4.00e-02 9.69e+01 ... (remaining 6324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1206 0.071 - 0.142: 357 0.142 - 0.212: 53 0.212 - 0.283: 4 0.283 - 0.354: 4 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 15 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB ILE H 119 " pdb=" CA ILE H 119 " pdb=" CG1 ILE H 119 " pdb=" CG2 ILE H 119 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CG LEU H 237 " pdb=" CB LEU H 237 " pdb=" CD1 LEU H 237 " pdb=" CD2 LEU H 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1621 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 297 " 0.041 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP B 297 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 297 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 297 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 297 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 297 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 297 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 130 " 0.008 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP H 130 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 130 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP H 130 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 130 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP H 130 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 130 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 130 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 130 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 130 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 163 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ASP B 163 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 163 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 164 " -0.017 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1916 2.76 - 3.30: 10033 3.30 - 3.83: 17865 3.83 - 4.37: 19716 4.37 - 4.90: 32970 Nonbonded interactions: 82500 Sorted by model distance: nonbonded pdb=" O PHE R 273 " pdb=" OG1 THR R 277 " model vdw 2.227 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.243 3.040 nonbonded pdb=" OG SER L 90 " pdb=" O THR L 97 " model vdw 2.245 3.040 nonbonded pdb=" O VAL R 157 " pdb=" OG1 THR R 160 " model vdw 2.251 3.040 ... (remaining 82495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.740 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.198 10680 Z= 0.652 Angle : 1.248 12.112 14498 Z= 0.683 Chirality : 0.066 0.354 1624 Planarity : 0.008 0.069 1841 Dihedral : 11.761 79.395 3835 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.65 % Allowed : 3.83 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.19), residues: 1318 helix: -2.37 (0.21), residues: 341 sheet: -1.91 (0.26), residues: 322 loop : -3.18 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.006 TRP B 297 HIS 0.027 0.005 HIS H 54 PHE 0.042 0.005 PHE A 215 TYR 0.041 0.004 TYR R 257 ARG 0.010 0.002 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8725 (m-40) cc_final: 0.7306 (t0) REVERT: A 304 GLN cc_start: 0.7462 (tt0) cc_final: 0.7188 (tm-30) REVERT: B 76 ASP cc_start: 0.8235 (p0) cc_final: 0.7855 (t0) REVERT: B 187 VAL cc_start: 0.7742 (t) cc_final: 0.7526 (t) REVERT: B 313 ASN cc_start: 0.8473 (t0) cc_final: 0.8100 (t0) REVERT: G 36 CYS cc_start: 0.8316 (m) cc_final: 0.7326 (m) REVERT: G 39 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8751 (mt-10) REVERT: L 34 THR cc_start: 0.8661 (m) cc_final: 0.8190 (p) REVERT: L 37 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7986 (mt-10) REVERT: H 172 TYR cc_start: 0.7838 (p90) cc_final: 0.7177 (p90) REVERT: R 39 MET cc_start: 0.7449 (mmp) cc_final: 0.7203 (mmm) REVERT: R 69 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7608 (ptp-170) REVERT: R 207 MET cc_start: 0.9121 (mmm) cc_final: 0.8705 (tpp) REVERT: R 253 MET cc_start: 0.9315 (mmm) cc_final: 0.8899 (mmm) REVERT: R 308 MET cc_start: 0.8799 (mtp) cc_final: 0.8479 (mtp) outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 0.2706 time to fit residues: 79.9629 Evaluate side-chains 119 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 204 GLN B 62 HIS B 91 HIS B 176 GLN B 295 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN L 235 ASN H 101 GLN H 191 HIS R 73 ASN R 100 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN R 312 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10680 Z= 0.208 Angle : 0.763 8.397 14498 Z= 0.405 Chirality : 0.046 0.232 1624 Planarity : 0.006 0.075 1841 Dihedral : 7.855 68.567 1488 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.52 % Allowed : 3.91 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1318 helix: -0.74 (0.26), residues: 329 sheet: -1.54 (0.27), residues: 321 loop : -2.68 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 82 HIS 0.007 0.002 HIS R 65 PHE 0.016 0.002 PHE A 215 TYR 0.030 0.002 TYR R 301 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8749 (m-40) cc_final: 0.7554 (t0) REVERT: A 24 ARG cc_start: 0.8534 (ppt170) cc_final: 0.8255 (ttp80) REVERT: A 304 GLN cc_start: 0.7388 (tt0) cc_final: 0.7078 (tm-30) REVERT: A 305 CYS cc_start: 0.7921 (m) cc_final: 0.7498 (t) REVERT: B 58 ILE cc_start: 0.8822 (mt) cc_final: 0.8188 (pt) REVERT: B 76 ASP cc_start: 0.8140 (p0) cc_final: 0.7935 (t0) REVERT: B 91 HIS cc_start: 0.6845 (m90) cc_final: 0.6474 (m170) REVERT: B 111 TYR cc_start: 0.8137 (m-10) cc_final: 0.7600 (m-10) REVERT: B 160 SER cc_start: 0.8674 (p) cc_final: 0.8190 (p) REVERT: B 187 VAL cc_start: 0.7382 (t) cc_final: 0.7086 (t) REVERT: B 313 ASN cc_start: 0.8420 (t0) cc_final: 0.8145 (t0) REVERT: G 36 CYS cc_start: 0.8157 (m) cc_final: 0.6588 (m) REVERT: G 39 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8667 (mt-10) REVERT: L 34 THR cc_start: 0.8760 (m) cc_final: 0.8305 (p) REVERT: L 37 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7865 (mt-10) REVERT: L 172 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8270 (mtmm) REVERT: L 190 ASP cc_start: 0.8096 (p0) cc_final: 0.7871 (p0) REVERT: H 22 GLN cc_start: 0.7762 (mp10) cc_final: 0.7475 (mp10) REVERT: H 172 TYR cc_start: 0.7756 (p90) cc_final: 0.7169 (p90) REVERT: R 69 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7341 (mpt-90) REVERT: R 183 MET cc_start: 0.8660 (mtm) cc_final: 0.8330 (mmm) REVERT: R 207 MET cc_start: 0.8972 (mmm) cc_final: 0.8624 (tpp) REVERT: R 253 MET cc_start: 0.9308 (mmm) cc_final: 0.8926 (mmt) REVERT: R 302 ASN cc_start: 0.8735 (m110) cc_final: 0.8167 (m110) REVERT: R 305 ILE cc_start: 0.9320 (pt) cc_final: 0.9001 (tt) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.2652 time to fit residues: 67.2418 Evaluate side-chains 126 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10680 Z= 0.197 Angle : 0.692 8.077 14498 Z= 0.367 Chirality : 0.045 0.205 1624 Planarity : 0.005 0.046 1841 Dihedral : 7.132 69.693 1488 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.43 % Allowed : 2.70 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.22), residues: 1318 helix: -0.38 (0.27), residues: 340 sheet: -1.22 (0.28), residues: 309 loop : -2.44 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 297 HIS 0.007 0.001 HIS R 65 PHE 0.035 0.002 PHE R 85 TYR 0.017 0.002 TYR A 287 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8820 (m-40) cc_final: 0.7332 (t0) REVERT: A 24 ARG cc_start: 0.8583 (ppt170) cc_final: 0.8238 (ttp80) REVERT: A 53 MET cc_start: 0.5060 (ttp) cc_final: 0.4826 (ttp) REVERT: A 188 HIS cc_start: 0.8351 (m-70) cc_final: 0.8145 (m-70) REVERT: A 305 CYS cc_start: 0.7806 (m) cc_final: 0.7377 (t) REVERT: B 58 ILE cc_start: 0.8840 (mt) cc_final: 0.8266 (pt) REVERT: B 111 TYR cc_start: 0.8146 (m-10) cc_final: 0.7664 (m-10) REVERT: B 252 LEU cc_start: 0.7839 (tt) cc_final: 0.7638 (tp) REVERT: B 325 MET cc_start: 0.7821 (tmm) cc_final: 0.7018 (tmm) REVERT: G 36 CYS cc_start: 0.7959 (m) cc_final: 0.7121 (m) REVERT: G 41 ARG cc_start: 0.8857 (mtt90) cc_final: 0.8227 (mtt90) REVERT: L 34 THR cc_start: 0.8873 (m) cc_final: 0.8379 (p) REVERT: L 37 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7851 (mt-10) REVERT: L 172 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8180 (mtmm) REVERT: L 190 ASP cc_start: 0.8038 (p0) cc_final: 0.7824 (p0) REVERT: H 172 TYR cc_start: 0.7759 (p90) cc_final: 0.7181 (p90) REVERT: R 69 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7431 (mtt90) REVERT: R 183 MET cc_start: 0.8684 (mtm) cc_final: 0.8341 (mmm) REVERT: R 189 ILE cc_start: 0.8566 (pt) cc_final: 0.8239 (mp) REVERT: R 253 MET cc_start: 0.9210 (mmm) cc_final: 0.8854 (mmt) REVERT: R 305 ILE cc_start: 0.9330 (pt) cc_final: 0.9072 (tt) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.2494 time to fit residues: 61.0020 Evaluate side-chains 126 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 119 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS L 115 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10680 Z= 0.177 Angle : 0.666 8.212 14498 Z= 0.350 Chirality : 0.045 0.235 1624 Planarity : 0.005 0.057 1841 Dihedral : 6.780 72.104 1488 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.35 % Allowed : 2.35 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.22), residues: 1318 helix: 0.00 (0.27), residues: 336 sheet: -1.02 (0.29), residues: 303 loop : -2.26 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 175 HIS 0.007 0.001 HIS R 211 PHE 0.021 0.002 PHE A 215 TYR 0.015 0.001 TYR A 287 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8769 (m-40) cc_final: 0.7367 (t0) REVERT: A 24 ARG cc_start: 0.8513 (ppt170) cc_final: 0.8162 (ttp80) REVERT: A 53 MET cc_start: 0.5120 (ttp) cc_final: 0.4901 (ttp) REVERT: A 242 ARG cc_start: 0.5432 (mtt-85) cc_final: 0.4584 (mmp-170) REVERT: A 304 GLN cc_start: 0.7310 (tt0) cc_final: 0.6977 (tp-100) REVERT: B 253 PHE cc_start: 0.6395 (m-80) cc_final: 0.6139 (m-80) REVERT: B 313 ASN cc_start: 0.8387 (t0) cc_final: 0.8052 (t0) REVERT: B 325 MET cc_start: 0.8182 (tmm) cc_final: 0.7215 (tmm) REVERT: G 31 MET cc_start: 0.7296 (ppp) cc_final: 0.6938 (tpp) REVERT: G 36 CYS cc_start: 0.7920 (m) cc_final: 0.7260 (m) REVERT: L 34 THR cc_start: 0.8874 (m) cc_final: 0.8284 (p) REVERT: L 37 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7724 (mt-10) REVERT: L 190 ASP cc_start: 0.8030 (p0) cc_final: 0.7799 (p0) REVERT: H 172 TYR cc_start: 0.7624 (p90) cc_final: 0.7039 (p90) REVERT: R 69 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7425 (mtt90) REVERT: R 163 MET cc_start: 0.8586 (mmm) cc_final: 0.8330 (mmm) REVERT: R 183 MET cc_start: 0.8701 (mtm) cc_final: 0.8390 (mmm) REVERT: R 189 ILE cc_start: 0.8599 (pt) cc_final: 0.8303 (mp) REVERT: R 207 MET cc_start: 0.8793 (tpp) cc_final: 0.8470 (tpp) REVERT: R 253 MET cc_start: 0.9187 (mmm) cc_final: 0.8816 (mmt) REVERT: R 305 ILE cc_start: 0.9331 (pt) cc_final: 0.9095 (tt) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2490 time to fit residues: 56.8710 Evaluate side-chains 116 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 239 ASN L 115 GLN L 116 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10680 Z= 0.268 Angle : 0.698 8.590 14498 Z= 0.368 Chirality : 0.045 0.205 1624 Planarity : 0.005 0.079 1841 Dihedral : 6.883 69.595 1488 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.35 % Allowed : 2.78 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.22), residues: 1318 helix: 0.06 (0.27), residues: 334 sheet: -1.07 (0.28), residues: 321 loop : -2.25 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 126 HIS 0.011 0.002 HIS B 54 PHE 0.017 0.002 PHE L 123 TYR 0.013 0.002 TYR A 287 ARG 0.009 0.001 ARG R 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8827 (m-40) cc_final: 0.7382 (t0) REVERT: A 24 ARG cc_start: 0.8655 (ppt170) cc_final: 0.8208 (ttp80) REVERT: A 53 MET cc_start: 0.5407 (ttp) cc_final: 0.5160 (ttp) REVERT: A 188 HIS cc_start: 0.8231 (m-70) cc_final: 0.8018 (m-70) REVERT: B 111 TYR cc_start: 0.8172 (m-10) cc_final: 0.7649 (m-10) REVERT: B 325 MET cc_start: 0.8209 (tmm) cc_final: 0.7312 (tmm) REVERT: G 35 LYS cc_start: 0.8186 (tptt) cc_final: 0.7887 (ptmt) REVERT: L 115 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6536 (pp30) REVERT: L 190 ASP cc_start: 0.8087 (p0) cc_final: 0.7880 (p0) REVERT: H 172 TYR cc_start: 0.7757 (p90) cc_final: 0.7153 (p90) REVERT: R 69 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7476 (mtt90) REVERT: R 183 MET cc_start: 0.8756 (mtm) cc_final: 0.8449 (mmm) REVERT: R 189 ILE cc_start: 0.8694 (pt) cc_final: 0.8354 (mp) REVERT: R 207 MET cc_start: 0.8961 (tpp) cc_final: 0.8675 (tpp) REVERT: R 253 MET cc_start: 0.9194 (mmm) cc_final: 0.8757 (mmt) REVERT: R 296 LYS cc_start: 0.8676 (mmpt) cc_final: 0.8308 (mtmm) REVERT: R 305 ILE cc_start: 0.9371 (pt) cc_final: 0.9072 (tt) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2661 time to fit residues: 54.7906 Evaluate side-chains 110 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10680 Z= 0.331 Angle : 0.758 9.835 14498 Z= 0.402 Chirality : 0.047 0.234 1624 Planarity : 0.005 0.056 1841 Dihedral : 7.065 68.394 1488 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.26 % Allowed : 1.65 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.22), residues: 1318 helix: -0.29 (0.26), residues: 338 sheet: -1.15 (0.28), residues: 318 loop : -2.31 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 126 HIS 0.008 0.002 HIS R 65 PHE 0.038 0.002 PHE L 123 TYR 0.016 0.002 TYR B 105 ARG 0.005 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8751 (ppt170) cc_final: 0.8263 (ttp80) REVERT: A 53 MET cc_start: 0.5624 (ttp) cc_final: 0.5317 (ttp) REVERT: A 188 HIS cc_start: 0.8450 (m-70) cc_final: 0.8072 (m-70) REVERT: A 198 MET cc_start: 0.8251 (mtp) cc_final: 0.7936 (mtm) REVERT: A 242 ARG cc_start: 0.5671 (mtt-85) cc_final: 0.4711 (mmp-170) REVERT: B 262 MET cc_start: 0.7409 (mmm) cc_final: 0.7191 (mmm) REVERT: B 313 ASN cc_start: 0.8411 (t0) cc_final: 0.8127 (p0) REVERT: B 325 MET cc_start: 0.8228 (tmm) cc_final: 0.7345 (tmm) REVERT: L 114 MET cc_start: 0.7318 (ttm) cc_final: 0.7057 (ttt) REVERT: H 109 ASP cc_start: 0.8250 (m-30) cc_final: 0.8045 (m-30) REVERT: H 172 TYR cc_start: 0.7805 (p90) cc_final: 0.7167 (p90) REVERT: R 69 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7473 (mtt90) REVERT: R 155 MET cc_start: 0.9337 (ppp) cc_final: 0.9113 (ppp) REVERT: R 207 MET cc_start: 0.8986 (tpp) cc_final: 0.8719 (tpp) REVERT: R 253 MET cc_start: 0.9220 (mmm) cc_final: 0.8693 (mmt) REVERT: R 305 ILE cc_start: 0.9354 (pt) cc_final: 0.9019 (tt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2446 time to fit residues: 45.9031 Evaluate side-chains 106 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.9990 chunk 14 optimal weight: 0.0170 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10680 Z= 0.228 Angle : 0.688 9.457 14498 Z= 0.363 Chirality : 0.045 0.210 1624 Planarity : 0.005 0.070 1841 Dihedral : 6.840 71.994 1488 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.26 % Allowed : 1.39 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.22), residues: 1318 helix: -0.06 (0.27), residues: 336 sheet: -1.10 (0.28), residues: 320 loop : -2.21 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 126 HIS 0.011 0.002 HIS B 54 PHE 0.034 0.002 PHE R 159 TYR 0.014 0.002 TYR H 113 ARG 0.005 0.001 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8738 (ppt170) cc_final: 0.8172 (ttp80) REVERT: A 188 HIS cc_start: 0.8377 (m-70) cc_final: 0.8083 (m-70) REVERT: A 242 ARG cc_start: 0.5751 (mtt-85) cc_final: 0.4737 (mmp-170) REVERT: B 313 ASN cc_start: 0.8511 (t0) cc_final: 0.8208 (p0) REVERT: B 325 MET cc_start: 0.8219 (tmm) cc_final: 0.7319 (tmm) REVERT: H 25 GLU cc_start: 0.8662 (mp0) cc_final: 0.8272 (mp0) REVERT: H 172 TYR cc_start: 0.7715 (p90) cc_final: 0.7061 (p90) REVERT: R 69 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7410 (mtt90) REVERT: R 155 MET cc_start: 0.9332 (ppp) cc_final: 0.9102 (ppp) REVERT: R 207 MET cc_start: 0.9007 (tpp) cc_final: 0.8732 (tpp) REVERT: R 253 MET cc_start: 0.9199 (mmm) cc_final: 0.8733 (mmt) REVERT: R 305 ILE cc_start: 0.9370 (pt) cc_final: 0.9051 (tt) REVERT: R 308 MET cc_start: 0.8990 (mtp) cc_final: 0.8673 (ttm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2529 time to fit residues: 50.3607 Evaluate side-chains 109 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10680 Z= 0.178 Angle : 0.661 8.237 14498 Z= 0.345 Chirality : 0.045 0.197 1624 Planarity : 0.005 0.053 1841 Dihedral : 6.599 72.508 1488 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.26 % Allowed : 0.96 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1318 helix: 0.17 (0.27), residues: 334 sheet: -0.98 (0.29), residues: 304 loop : -2.07 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.008 0.001 HIS B 54 PHE 0.039 0.002 PHE R 159 TYR 0.015 0.001 TYR B 59 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8755 (m-40) cc_final: 0.7323 (t0) REVERT: A 24 ARG cc_start: 0.8703 (ppt170) cc_final: 0.8116 (ttp80) REVERT: A 188 HIS cc_start: 0.8401 (m-70) cc_final: 0.7931 (m-70) REVERT: A 242 ARG cc_start: 0.5790 (mtt-85) cc_final: 0.4792 (mmp-170) REVERT: B 111 TYR cc_start: 0.8023 (m-10) cc_final: 0.7541 (m-10) REVERT: B 313 ASN cc_start: 0.8409 (t0) cc_final: 0.8142 (t0) REVERT: B 325 MET cc_start: 0.8198 (tmm) cc_final: 0.7263 (tmm) REVERT: G 41 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8339 (mtt90) REVERT: L 114 MET cc_start: 0.6884 (ttm) cc_final: 0.6605 (ttm) REVERT: L 190 ASP cc_start: 0.8174 (p0) cc_final: 0.7922 (p0) REVERT: H 172 TYR cc_start: 0.7636 (p90) cc_final: 0.7060 (p90) REVERT: H 196 LEU cc_start: 0.8497 (tp) cc_final: 0.8267 (tt) REVERT: R 69 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7163 (mpt-90) REVERT: R 155 MET cc_start: 0.9331 (ppp) cc_final: 0.9079 (ppp) REVERT: R 207 MET cc_start: 0.8977 (tpp) cc_final: 0.8718 (tpp) REVERT: R 253 MET cc_start: 0.9159 (mmm) cc_final: 0.8692 (mmt) REVERT: R 302 ASN cc_start: 0.8939 (t160) cc_final: 0.8486 (t0) REVERT: R 305 ILE cc_start: 0.9355 (pt) cc_final: 0.9032 (tt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2521 time to fit residues: 51.8339 Evaluate side-chains 109 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.0030 chunk 110 optimal weight: 0.1980 chunk 117 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 overall best weight: 0.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10680 Z= 0.164 Angle : 0.657 8.025 14498 Z= 0.344 Chirality : 0.044 0.189 1624 Planarity : 0.004 0.053 1841 Dihedral : 6.371 76.305 1488 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.26 % Allowed : 0.43 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.23), residues: 1318 helix: 0.43 (0.28), residues: 334 sheet: -0.74 (0.29), residues: 311 loop : -1.97 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 175 HIS 0.005 0.001 HIS R 65 PHE 0.037 0.001 PHE R 159 TYR 0.013 0.001 TYR B 264 ARG 0.009 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8574 (mmp) cc_final: 0.7463 (tmm) REVERT: A 22 ASN cc_start: 0.8732 (m-40) cc_final: 0.7397 (t0) REVERT: A 24 ARG cc_start: 0.8712 (ppt170) cc_final: 0.8200 (ttp80) REVERT: A 188 HIS cc_start: 0.8355 (m-70) cc_final: 0.7911 (m-70) REVERT: B 253 PHE cc_start: 0.6290 (m-80) cc_final: 0.6011 (m-80) REVERT: B 262 MET cc_start: 0.6747 (mmm) cc_final: 0.6517 (mmm) REVERT: B 313 ASN cc_start: 0.8439 (t0) cc_final: 0.8148 (t0) REVERT: B 325 MET cc_start: 0.8197 (tmm) cc_final: 0.6580 (tmm) REVERT: G 41 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8345 (mtt90) REVERT: L 190 ASP cc_start: 0.8116 (p0) cc_final: 0.7879 (p0) REVERT: H 172 TYR cc_start: 0.7661 (p90) cc_final: 0.7102 (p90) REVERT: H 196 LEU cc_start: 0.8478 (tp) cc_final: 0.8229 (tt) REVERT: H 198 GLN cc_start: 0.8812 (tp40) cc_final: 0.8390 (tp40) REVERT: R 69 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7130 (mpt-90) REVERT: R 155 MET cc_start: 0.9349 (ppp) cc_final: 0.9098 (ppp) REVERT: R 207 MET cc_start: 0.8955 (tpp) cc_final: 0.8730 (tpp) REVERT: R 253 MET cc_start: 0.9142 (mmm) cc_final: 0.8624 (mmt) REVERT: R 305 ILE cc_start: 0.9416 (pt) cc_final: 0.9067 (tt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2518 time to fit residues: 54.4694 Evaluate side-chains 112 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10680 Z= 0.189 Angle : 0.662 8.207 14498 Z= 0.346 Chirality : 0.044 0.191 1624 Planarity : 0.005 0.055 1841 Dihedral : 6.328 77.341 1488 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.23), residues: 1318 helix: 0.48 (0.28), residues: 333 sheet: -0.81 (0.28), residues: 325 loop : -2.01 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 175 HIS 0.006 0.001 HIS B 54 PHE 0.034 0.002 PHE R 159 TYR 0.011 0.001 TYR R 178 ARG 0.010 0.001 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8783 (m-40) cc_final: 0.7406 (t0) REVERT: A 24 ARG cc_start: 0.8717 (ppt170) cc_final: 0.8212 (ttp80) REVERT: A 188 HIS cc_start: 0.8363 (m-70) cc_final: 0.8044 (m-70) REVERT: A 304 GLN cc_start: 0.7368 (tt0) cc_final: 0.7070 (tp-100) REVERT: B 111 TYR cc_start: 0.7997 (m-10) cc_final: 0.7524 (m-10) REVERT: B 313 ASN cc_start: 0.8495 (t0) cc_final: 0.8218 (t0) REVERT: B 325 MET cc_start: 0.8542 (tmm) cc_final: 0.7885 (tmm) REVERT: G 41 ARG cc_start: 0.8688 (mtt90) cc_final: 0.8359 (mtt90) REVERT: L 190 ASP cc_start: 0.8186 (p0) cc_final: 0.7938 (p0) REVERT: H 112 MET cc_start: 0.7810 (tpt) cc_final: 0.7368 (tpt) REVERT: H 172 TYR cc_start: 0.7468 (p90) cc_final: 0.6982 (p90) REVERT: H 196 LEU cc_start: 0.8461 (tp) cc_final: 0.8193 (tt) REVERT: H 198 GLN cc_start: 0.8849 (tp40) cc_final: 0.8429 (tp40) REVERT: R 69 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7163 (mpt-90) REVERT: R 155 MET cc_start: 0.9347 (ppp) cc_final: 0.9075 (ppp) REVERT: R 207 MET cc_start: 0.9006 (tpp) cc_final: 0.8719 (tpp) REVERT: R 253 MET cc_start: 0.9165 (mmm) cc_final: 0.8605 (mmt) REVERT: R 305 ILE cc_start: 0.9411 (pt) cc_final: 0.9055 (tt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2503 time to fit residues: 50.8675 Evaluate side-chains 112 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.078191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063544 restraints weight = 65848.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062952 restraints weight = 36712.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063810 restraints weight = 33963.528| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10680 Z= 0.279 Angle : 0.719 8.477 14498 Z= 0.378 Chirality : 0.045 0.204 1624 Planarity : 0.005 0.056 1841 Dihedral : 6.628 76.803 1488 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.26 % Allowed : 0.17 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1318 helix: 0.29 (0.28), residues: 334 sheet: -0.83 (0.28), residues: 333 loop : -2.09 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 297 HIS 0.008 0.002 HIS R 65 PHE 0.040 0.002 PHE L 61 TYR 0.016 0.002 TYR H 202 ARG 0.009 0.001 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.30 seconds wall clock time: 42 minutes 25.07 seconds (2545.07 seconds total)